Mosquitoes are vectors of many parasitic and viral diseases that continue to burden the global public health system. The innate immune system of insects is the first line of defense against invading pathogens. This system is governed by two major pathways, Toll, and IMD pathways. This dissertation involves the investigation of these pathways. Aim 1 involves the exploration of the Toll and PPO activation pathway in response to pathogen invasion. Aim 2 seeks to investigate the components of the IMD pathway and lastly, Aim 3 provides a comparative genomic study of the mosquito immune system. The results of the first aim identified an interleukin receptor associated kinase (IRAK), IRAK4, in the mosquito, Aedes aegyti. Furthermore, it was found that IRAK4 serves an important immune function in the Toll immune pathway. Addtionally, several cytoplasmic components of the IMD pathway were identified including PGRPLC, IMD, IKKβ, and FADD (Aim 2).